Single-Color Review and Spectral Unmixing Made Easier

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Documentation for package ‘spectreasy’ version 1.0.0

• DESCRIPTION file
• Package NEWS
• Package README

Help Pages

.calculate_control_collinearity	Calculate exact fixed-model diagnostics for a control reference matrix.
.calculate_control_uds_use	Calculate empirical USE and matched fixed-model SIF ratios.
.calculate_fixed_collinearity_vif_magnitude_sif	Calculate exact VIF magnitude and SIF values for one fixed effective model.
adjust_control_reference	Adjust a completed control reference matrix
build_reference_matrix	Build a Reference Matrix from Single-Color Controls
calculate_af_repertoire_qc_metrics	Calculate deterministic AF-repertoire diagnostics
calculate_control_qc_metrics	Calculate deterministic event-level SCC quality metrics
calculate_cosine_similarity_matrix	Calculate a cosine-similarity matrix
calculate_nps	Calculate the negative-tail MAD proxy (historically NPS)
calculate_similarity_matrix	Calculate a cosine-similarity matrix (legacy name)
calculate_unstained_robust_spread	Calculate robust spread for unmixed unstained-control coefficients
calc_residuals	Calculate unmixing residuals
check_for_updates	Check for and install Spectreasy updates
collect_control_report_bundle	Collect a modular control QC report bundle
collect_control_report_data	Collect control QC report data
collect_sample_report_bundle	Collect a modular sample QC report bundle
collect_sample_report_data	Collect sample QC report data
control_qc_modules_default	Default control QC modules
control_qc_reports_default	Default control QC reports
create_control_file	Create spectreasy Control File
derive_unmixing_matrix	Derive Unmixing Matrix from Reference Matrix
export_qc_report_pdf	Export an existing Spectreasy HTML QC report to PDF
extract_control_spectra	Automatically Gate and Extract Control Spectra
gate_controls	Gate Single-Color Controls Interactively
get_control_spectra	Get Previously Extracted Control Spectra
get_fluorophore_patterns	Get Standard Fluorophore Filename Patterns
get_sorted_detectors	Get Sorted Detectors by Laser and Wavelength
inspect_fcs_provenance	Inspect scientific provenance embedded in FCS files
inspect_spectreasy_provenance	Inspect a portable provenance envelope produced by Spectreasy
install_qc_dependencies	Ensure the CompensAID QC dependency
launch	Launch the Spectreasy GUI
plot_compensaid_matrix	Plot a directional CompensAID SSI matrix
plot_compensaid_pair	Plot one CompensAID directional marker pair
plot_control_compensaid_matrix	Plot a control directional SSI matrix
plot_cosine_similarity_matrix	Plot a cosine-similarity matrix
plot_nps	Plot historical negative-tail spread
plot_sample_rms_residuals	Plot Overall Detector Reconstruction Error Across Samples
plot_similarity_matrix	Plot a cosine-similarity matrix (legacy name)
plot_spectra	Plot Spectral Overlays
plot_unmixing_matrix	Plot Unmixing Matrix
plot_unmixing_scatter_matrix	Plot NxN Unmixing Scatter Matrix
qc_controls	Generate modular control QC reports
qc_samples	Generate modular sample QC reports
read_control_extraction	Read Extracted Control Spectra for Direct R Unmixing
read_control_reference	Read a completed control reference
read_sample_run_manifest	Read a persisted sample-run manifest.
render_qc_html_report	Render a Spectreasy QC report object as HTML
sample_qc_modules_default	Default sample QC modules
sample_qc_reports_default	Default sample QC reports
save_unmixing_matrix	Save Unmixing Matrix to CSV
spectreasy_capabilities	Report stable behavioral capabilities
spectreasy_example_data	Download and cache the spectreasy example FCS files
spectreasy_gui	Launch the Spectreasy GUI
spectreasy_gui_runtime	Create a host-composable Spectreasy GUI runtime session
spectreasy_native_map_data_to_codes_cpp	Map data onto a trained SOM codebook (OpenMP-accelerated)
spectreasy_native_som_train_batch_cpp	Train a Self-Organizing Map with batch updates (OpenMP-accelerated)
supported_cytometers	Supported Cytometers
unmix_controls	Unmix Single-Color Controls
unmix_samples	Unmix Experimental Samples
update_spectreasy	Check for and install Spectreasy updates
validate_control_file_mapping	Validate SCC Control Mapping Before Unmixing
validate_sample_run	Validate a persisted sample-run manifest and its output provenance.
verify_spectreasy_provenance	Verify portable provenance checksums for Spectreasy artifacts